Gaussian Accelerated Molecular Dynamics Simulations Investigation on the Mechanism of Angiotensin-Converting Enzyme (ACE) C-Domain Inhibition by Dipeptides

Computational exploration of naturally derived peptides inhibitory mechanisms against ACE enzyme, from interactions to structural-dynamics

Naturally derived peptides have gained significant attention because of their potential to reduce blood pressure. These peptides can be derived from various sources, including snake venom, marine organisms, cow's milk, seahorses, and plants. Investigating the underlying mechanisms of these peptides in lowering blood pressure is crucial for replacing synthetic drugs currently in use. In this regard, we conducted in silico studies, such as molecular docking, classical molecular dynamics (MD) simulations, and QM/MM simulation methods, on two naturally derived peptides (PAGPRGPA and WALKGYK) and Angiotensin II (ANGII) as the enzyme substrates for binding to sACE. The results of 500 ns MD calculations showed that the WALKGYK peptide occupies the ACE binding site, similar to the ANGII and BPPb peptides, two distinguished C-domain-specific inhibitors. Furthermore, QM/MM calculations demonstrated that no peptide bond cleavage was mediated by Zn2+ at the catalytic site of the peptides. However, during the 500 ns MD simulation, the backbone oxygens of LYS4 and GLY5 of the WALKGYK peptides were tightly coordinated to the Zn2+ ion. Free energy calculations also confirmed the higher affinity of the WALKGYK peptides for binding to sACE. In addition, structural analysis correlation showed a different pattern in PAGPRGPA compared to WALKGYK and ANGII. Despite the similarity of the peptide PAGPRGPA to typical ACE peptide inhibitors with hydrophobic ends, the electrostatic composition of the WALKGYK peptide showed a higher tendency towards ACE inhibition. Therefore, peptide residue compositions, such as WALKGYK, can be considered for designing new inhibitors with fewer side effects for sACE C-terminal inhibitors.

Ace Deficiency Induces Intestinal Inflammation in Zebrafish

Inflammatory bowel disease (IBD) is a nonspecific chronic inflammatory disease resulting from an immune disorder in the intestine that is prone to relapse and incurable. The understanding of the pathogenesis of IBD remains unclear. In this study, we found that ace (angiotensin-converting enzyme), expressed abundantly in the intestine, plays an important role in IBD. The deletion of ace in zebrafish caused intestinal inflammation with increased expression of the inflammatory marker genes interleukin 1 beta (il1b), matrix metallopeptidase 9 (mmp9), myeloid-specific peroxidase (mpx), leukocyte cell-derived chemotaxin-2-like (lect2l), and chemokine (C-X-C motif) ligand 8b (cxcl8b). Moreover, the secretion of mucus in the ace-/- mutants was significantly higher than that in the wild-type zebrafish, validating the phenotype of intestinal inflammation. This was further confirmed by the IBD model constructed using dextran sodium sulfate (DSS), in which the mutant zebrafish had a higher susceptibility to enteritis. Our study reveals the role of ace in intestinal homeostasis, providing a new target for potential therapeutic interventions.

Study on the Mechanism of Interaction between Dipeptidyl Peptidase 4 and Inhibitory Peptides Based on Gaussian Accelerated Molecular Dynamic Simulation

Dipeptidyl peptidase 4 (DPP4) inhibitors can effectively inhibit the activity of DPP4, increasing the concentrations of glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP), which allows for them to effectively contribute to the reduction of blood sugar levels. Leu-Pro-Ala-Val-Thr-Ile-Arg (LPAVTIR) and Leu-Pro-Pro-Glu-His-Asp-Trp-Arg (LPPEHDWR) were the two peptides with the strongest inhibitory activity against DPP4 selected from silkworm pupa proteins. In this study, four systems were established: Apo (ligand-free DPP4), IPI (IPI-bound DPP4), LPAVTIR (LPAVTIR-bound DPP4), LPPEHDWR (LPPEHDWR-bound DPP4), and Gaussian accelerated molecular dynamic (GaMD) simulation was conducted to investigate the mechanism of action of two inhibitory peptides binding to DPP4. Our study revealed that the LPAVTIR peptide possessed a more stable structure and exhibited a tighter binding to the Ser630 active site in DPP4, thus exhibiting a favorable competitive inhibition effect. In contrast, the LPPEHDWR peptide caused the horizontal α-helix (residues 201-215) composed of Glu205 and Glu206 residues in DPP4 to disappear. The spatial arrangement of active sites Ser630 relative to Glu205 and Glu206 was disrupted, resulting in enzyme inactivation. Moreover, the size of the substrate channel and cavity volume was significantly reduced after the binding of the inhibitory peptide to the protein, which was an important factor in the inhibition of the enzyme activity. A similar effect was also found from IPI (our positive control). By stabilizing the active site of DPP4, the IPI peptide induced the disappearance of the horizontal α-helix and a notable reduction in the active cavity volume. In conclusion, our study provided a solid theoretical foundation for the inhibitory mechanisms of IPI, LPAVTIR, and LPPEHDWR on DPP4, offering valuable insights for advancing the development of drug targets for type 2 diabetes.

Antihypertensive Effect, ACE Inhibitory Activity, and Stability of Umami Peptides from Yeast Extract

Bioactive peptides from foods have garnered considerable attention as viable supplements for hypertensive patients. Herein, the antihypertensive effect and mechanism of umami peptides from yeast extract were investigated based on the pharmacophore model, simulated digestion, spontaneously hypertensive rat (SHR) model, and molecular docking. Notably, umami peptide LLLLPKP exhibited favorable angiotensin I-converting enzyme (ACE) inhibitory activity (IC50 = 10.22 μM) in vitro and regulated blood pressure in the SHR model with excellent durability. Remarkably, LLLLPKP showed the highest Fitvalue (4.022) of the pharmacophore model, indicating its similar pharmacological effects as ACE inhibitors. During the simulated gastrointestinal digestion, the ACE inhibition rate of LLLLPKP was merely reduced by 5.89%, but it was enzymatically cleaved into 14 peptide segments. The C-terminal sequence comprising L (4), P (5), K (6), and P (7) exhibited robust stability and a notable presence within the peptide segments postdigestion. Meanwhile, according to molecular docking, these four residues within LLLLPKP were responsible for all interactions with key sites within active pockets S1 and S2 and the active pocket of Zn2+. In light of these findings, LLLLPKP is a highly promising antihypertensive peptide. Developing this umami peptide with antihypertensive effects holds substantial importance for the long-term treatment of hypertension.

Revealing the Sequence Characteristics and Molecular Mechanisms of ACE Inhibitory Peptides by Comprehensive Characterization of 160,000 Tetrapeptides

Chronic diseases, such as hypertension, cause great harm to human health. Conventional drugs have promising therapeutic effects, but also cause significant side effects. Food-sourced angiotensin-converting enzyme (ACE) inhibitory peptides are an excellent therapeutic alternative to pharmaceuticals, as they have fewer side effects. However, there is no systematic and effective screening method for ACE inhibitory peptides, and the lack of understanding of the sequence characteristics and molecular mechanism of these inhibitory peptides poses a major obstacle to the development of ACE inhibitory peptides. Through systematically calculating the binding effects of 160,000 tetrapeptides with ACE by molecular docking, we found that peptides with Tyr, Phe, His, Arg, and especially Trp were the characteristic amino acids of ACE inhibitory peptides. The tetrapeptides of WWNW, WRQF, WFRV, YYWK, WWDW, and WWTY rank in the top 10 peptides exhibiting significantly high ACE inhibiting behaviors, with IC₅₀ values between 19.98 ± 8.19 μM and 36.76 ± 1.32 μM. Salt bridges, π-π stacking, π-cations, and hydrogen bonds contributed to the high binding characteristics of the inhibitors and ACE. Introducing eight Trp into rabbit skeletal muscle protein (no Trp in wide sequence) endowed the protein with a more than 90% ACE inhibition rate, further suggesting that meat with a high content of Trp could have potential utility in hypertension regulation. This study provides a clear direction for the development and screening of ACE inhibitory peptides.

A comprehensive insight into the effects of caffeic acid (CA) on pepsin: Multi-spectroscopy and MD simulations methods

The interaction between caffeic acid (CA) and pepsin was investigated using multi-spectroscopy approaches and molecular dynamic simulations (MDS). The effects of CA on the structure, stability, and activity of pepsin were studied. Fluorescence emission spectra and UV-vis absorption peaks all represented the static quenching mechanism of pepsin by CA. Moreover, the fluorescence spectra displayed that the interaction of CA exposed the tryptophan chromophores of pepsin to a more hydrophilic micro-environment. Consistent with the simulation results, thermodynamic parameters revealed that CA was bound to pepsin with a high binding affinity. The Van der Waals force and Hydrogen bond interaction were the dominant driving forces during the binding process. The circular dichroism (CD) spectroscopy analysis showed that the CA binding to pepsin decreased the contents of α-Helix and Random Coil but increased the content of β-sheet in the pepsin structure. Accordingly, MD simulations confirmed all the experimental results. As a result, CA is considered an inhibitor with adverse effects on pepsin activity.

Exploration of the Product Specificity of chitosanase CsnMY002 and Mutants Using Molecular Dynamics Simulations

Chitosanase CsnMY002 is a new type of enzyme isolated from Bacillus subtilis that is used to prepare chitosan oligosaccharide. Although mutants G21R and G21K could increase Chitosan yield and thus increase the commercial value of the final product, the mechanism by which this happens is not known. Herein, we used molecular dynamics simulations to explore the conformational changes in CsnMY002 wild type and mutants when they bind substrates. The binding of substrate changed the conformation of protein, stretching and deforming the active and catalytic region. Additionally, the mutants caused different binding modes and catalysis, resulting in different degrees of polymerization of the final Chitooligosaccharide degradation product. Finally, Arg37, Ile145 ~ Gly148 and Trp204 are important catalytic residues of CsnMY002. Our study provides a basis for the engineering of chitosanases.